In the plots below, “red” color represents read depth of sample and “blue” color represents read depth of wild-type ie ancestral strain with GFp.

# Rscript -e "library(knitr); knit('analyzing_for_CNVs.Rmd')" -p <pindel output .txt> -c <cnvnator output .txt> -l <lumpy output .txt> -r <read depth .txt file>
# This will out put a .md file and a directory named "figure" in your working directory
# To view this .md (which is similar to .html file genearted by Rmarkdown, make sure that the .html and corresponding "figures" folder is in the same directory

# Obtain read depth file for wild type before starting analysis
library(optparse)
library(knitr)
## [1] "Mean Read Depth:"
## [1] 45.4716
## [1] "Deletion:Cnvnator"
##      svtype     chrom.1  start    end size normRDsignal
## 6  deletion NC_001134.8 694501 695100  600         0.13
## 8  deletion NC_001135.5  56821  57360  540         0.15
## 9  deletion NC_001135.5 148621 151560 2940         0.01
## 10 deletion NC_001135.5 205561 206160  600         0.13
## 17 deletion NC_001139.9   2221   2580  360         0.02
## 18 deletion NC_001139.9  89281  90060  780         0.11
## 33 deletion NC_001143.9  15781  16320  540         0.07
## [1] 1
##     svtype     chrom.1  start    end size normRDsignal
## 6 deletion NC_001134.8 694501 695100  600         0.13

## [1] 2
##     svtype     chrom.1 start   end size normRDsignal
## 8 deletion NC_001135.5 56821 57360  540         0.15

## [1] 3
##     svtype     chrom.1  start    end size normRDsignal
## 9 deletion NC_001135.5 148621 151560 2940         0.01

## [1] 4
##      svtype     chrom.1  start    end size normRDsignal
## 10 deletion NC_001135.5 205561 206160  600         0.13

## [1] 5
##      svtype     chrom.1 start  end size normRDsignal
## 17 deletion NC_001139.9  2221 2580  360         0.02

## [1] 6
##      svtype     chrom.1 start   end size normRDsignal
## 18 deletion NC_001139.9 89281 90060  780         0.11

## [1] 7
##      svtype     chrom.1 start   end size normRDsignal
## 33 deletion NC_001143.9 15781 16320  540         0.07

## [1] "Deletion:Lumpy"
##    svtype      chrom.1  start    end size
## 1     DEL NC_001136.10 383817 384080 -263
## 10    DEL  NC_001140.6  79753  80184 -431
## [1] 1
##   svtype      chrom.1  start    end size
## 1    DEL NC_001136.10 383817 384080 -263

## [1] 2
##    svtype     chrom.1 start   end size
## 10    DEL NC_001140.6 79753 80184 -431

## [1] "Deletion:Pindel"
##     svtype     chrom.1  start    end size supporting.reads
## 169      D NC_001144.5 457786 466925 9138               28
## [1] 1
##     svtype     chrom.1  start    end size supporting.reads
## 169      D NC_001144.5 457786 466925 9138               28

## [1] "Duplication:Cnvnator"
##          svtype      chrom.1   start     end  size normRDsignal
## 80  duplication  NC_001133.9  162121  165900  3780         2.30
## 83  duplication  NC_001134.8  222601  225000  2400         2.27
## 84  duplication  NC_001134.8  259861  264120  4260         2.02
## 93  duplication NC_001136.10  527881  538380 10500         1.99
## 94  duplication NC_001136.10  647461  651120  3660         2.23
## 100 duplication NC_001136.10  987361  992340  4980         2.34
## 101 duplication NC_001136.10 1095841 1101540  5700         2.08
## 102 duplication NC_001136.10 1206961 1212240  5280         2.56
## 105 duplication  NC_001137.3  443581  449040  5460         2.63
## 106 duplication  NC_001137.3  493381  498360  4980         2.01
## 117 duplication  NC_001139.9  535801  541560  5760         2.51
## 118 duplication  NC_001139.9  563821  568200  4380         1.90
## 122 duplication  NC_001140.6   40321   91080 50760         4.75
## 123 duplication  NC_001140.6  212461  219660  7200         2.64
## 127 duplication  NC_001140.6  544261  548460  4200         2.06
## 134 duplication  NC_001142.9  111541  113160  1620         1.91
## 136 duplication  NC_001142.9  472501  483840 11340         2.28
## 141 duplication  NC_001143.9  650641  651540   900         2.78
## 144 duplication  NC_001144.5  217801  220080  2280         2.30
## 146 duplication  NC_001144.5  451441  472560 21120        31.59
## 147 duplication  NC_001144.5  476341  481860  5520         2.37
## 149 duplication  NC_001144.5  593401  596700  3300         2.57
## 150 duplication  NC_001144.5  649981  655980  6000         2.22
## 154 duplication  NC_001145.3  184261  190020  5760         2.24
## 155 duplication  NC_001145.3  196621  202080  5460         2.54
## 160 duplication  NC_001146.8   24661   26940  2280         1.86
## 162 duplication  NC_001146.8   97321  100860  3540         2.37
## 165 duplication  NC_001146.8  520201  524280  4080         1.98
## 170 duplication  NC_001147.6  117961  123060  5100         2.75
## 171 duplication  NC_001147.6  594901  599940  5040         2.13
## 175 duplication  NC_001148.4   54961   61080  6120         2.22
## 181 duplication  NC_001148.4  804841  810240  5400         2.16
## 182 duplication  NC_001148.4  844501  856260 11760         2.13
## [1] 1
##         svtype     chrom.1  start    end size normRDsignal
## 80 duplication NC_001133.9 162121 165900 3780          2.3

## [1] 2
##         svtype     chrom.1  start    end size normRDsignal
## 83 duplication NC_001134.8 222601 225000 2400         2.27

## [1] 3
##         svtype     chrom.1  start    end size normRDsignal
## 84 duplication NC_001134.8 259861 264120 4260         2.02

## [1] 4
##         svtype      chrom.1  start    end  size normRDsignal
## 93 duplication NC_001136.10 527881 538380 10500         1.99

## [1] 5
##         svtype      chrom.1  start    end size normRDsignal
## 94 duplication NC_001136.10 647461 651120 3660         2.23

## [1] 6
##          svtype      chrom.1  start    end size normRDsignal
## 100 duplication NC_001136.10 987361 992340 4980         2.34

## [1] 7
##          svtype      chrom.1   start     end size normRDsignal
## 101 duplication NC_001136.10 1095841 1101540 5700         2.08

## [1] 8
##          svtype      chrom.1   start     end size normRDsignal
## 102 duplication NC_001136.10 1206961 1212240 5280         2.56

## [1] 9
##          svtype     chrom.1  start    end size normRDsignal
## 105 duplication NC_001137.3 443581 449040 5460         2.63

## [1] 10
##          svtype     chrom.1  start    end size normRDsignal
## 106 duplication NC_001137.3 493381 498360 4980         2.01

## [1] 11
##          svtype     chrom.1  start    end size normRDsignal
## 117 duplication NC_001139.9 535801 541560 5760         2.51

## [1] 12
##          svtype     chrom.1  start    end size normRDsignal
## 118 duplication NC_001139.9 563821 568200 4380          1.9

## [1] 13
##          svtype     chrom.1 start   end  size normRDsignal
## 122 duplication NC_001140.6 40321 91080 50760         4.75

## [1] 14
##          svtype     chrom.1  start    end size normRDsignal
## 123 duplication NC_001140.6 212461 219660 7200         2.64

## [1] 15
##          svtype     chrom.1  start    end size normRDsignal
## 127 duplication NC_001140.6 544261 548460 4200         2.06

## [1] 16
##          svtype     chrom.1  start    end size normRDsignal
## 134 duplication NC_001142.9 111541 113160 1620         1.91

## [1] 17
##          svtype     chrom.1  start    end  size normRDsignal
## 136 duplication NC_001142.9 472501 483840 11340         2.28

## [1] 18
##          svtype     chrom.1  start    end size normRDsignal
## 141 duplication NC_001143.9 650641 651540  900         2.78

## [1] 19
##          svtype     chrom.1  start    end size normRDsignal
## 144 duplication NC_001144.5 217801 220080 2280          2.3

## [1] 20
##          svtype     chrom.1  start    end  size normRDsignal
## 146 duplication NC_001144.5 451441 472560 21120        31.59

## [1] 21
##          svtype     chrom.1  start    end size normRDsignal
## 147 duplication NC_001144.5 476341 481860 5520         2.37

## [1] 22
##          svtype     chrom.1  start    end size normRDsignal
## 149 duplication NC_001144.5 593401 596700 3300         2.57

## [1] 23
##          svtype     chrom.1  start    end size normRDsignal
## 150 duplication NC_001144.5 649981 655980 6000         2.22

## [1] 24
##          svtype     chrom.1  start    end size normRDsignal
## 154 duplication NC_001145.3 184261 190020 5760         2.24

## [1] 25
##          svtype     chrom.1  start    end size normRDsignal
## 155 duplication NC_001145.3 196621 202080 5460         2.54

## [1] 26
##          svtype     chrom.1 start   end size normRDsignal
## 160 duplication NC_001146.8 24661 26940 2280         1.86

## [1] 27
##          svtype     chrom.1 start    end size normRDsignal
## 162 duplication NC_001146.8 97321 100860 3540         2.37

## [1] 28
##          svtype     chrom.1  start    end size normRDsignal
## 165 duplication NC_001146.8 520201 524280 4080         1.98

## [1] 29
##          svtype     chrom.1  start    end size normRDsignal
## 170 duplication NC_001147.6 117961 123060 5100         2.75

## [1] 30
##          svtype     chrom.1  start    end size normRDsignal
## 171 duplication NC_001147.6 594901 599940 5040         2.13

## [1] 31
##          svtype     chrom.1 start   end size normRDsignal
## 175 duplication NC_001148.4 54961 61080 6120         2.22

## [1] 32
##          svtype     chrom.1  start    end size normRDsignal
## 181 duplication NC_001148.4 804841 810240 5400         2.16

## [1] 33
##          svtype     chrom.1  start    end  size normRDsignal
## 182 duplication NC_001148.4 844501 856260 11760         2.13

## [1] "Duplication:Lumpy"
##    svtype     chrom.1  start    end size
## 13    DUP NC_001145.3 908138 908616  478
## [1] 1
##    svtype     chrom.1  start    end size
## 13    DUP NC_001145.3 908138 908616  478

## [1] "Duplication:Pindel"
##     svtype     chrom.1  start    end size supporting.reads
## 278     TD NC_001144.5 457786 466923 9136               22
## 279     TD NC_001144.5 457786 466925 9138               14
## [1] 1
##     svtype     chrom.1  start    end size supporting.reads
## 278     TD NC_001144.5 457786 466923 9136               22

## [1] 2
##     svtype     chrom.1  start    end size supporting.reads
## 279     TD NC_001144.5 457786 466925 9138               14

pindel_del_filtered
##     svtype     chrom.1  start    end size supporting.reads
## 169      D NC_001144.5 457786 466925 9138               28
cnv_del_filtered
##      svtype     chrom.1  start    end size normRDsignal
## 6  deletion NC_001134.8 694501 695100  600         0.13
## 8  deletion NC_001135.5  56821  57360  540         0.15
## 9  deletion NC_001135.5 148621 151560 2940         0.01
## 10 deletion NC_001135.5 205561 206160  600         0.13
## 17 deletion NC_001139.9   2221   2580  360         0.02
## 18 deletion NC_001139.9  89281  90060  780         0.11
## 33 deletion NC_001143.9  15781  16320  540         0.07
lumpy_del_filtered
##    svtype      chrom.1  start    end size
## 1     DEL NC_001136.10 383817 384080 -263
## 10    DEL  NC_001140.6  79753  80184 -431
pindel_dup_filtered
##     svtype     chrom.1  start    end size supporting.reads
## 278     TD NC_001144.5 457786 466923 9136               22
## 279     TD NC_001144.5 457786 466925 9138               14
cnv_dup_filtered
##          svtype      chrom.1   start     end  size normRDsignal
## 80  duplication  NC_001133.9  162121  165900  3780         2.30
## 83  duplication  NC_001134.8  222601  225000  2400         2.27
## 84  duplication  NC_001134.8  259861  264120  4260         2.02
## 93  duplication NC_001136.10  527881  538380 10500         1.99
## 94  duplication NC_001136.10  647461  651120  3660         2.23
## 100 duplication NC_001136.10  987361  992340  4980         2.34
## 101 duplication NC_001136.10 1095841 1101540  5700         2.08
## 102 duplication NC_001136.10 1206961 1212240  5280         2.56
## 105 duplication  NC_001137.3  443581  449040  5460         2.63
## 106 duplication  NC_001137.3  493381  498360  4980         2.01
## 117 duplication  NC_001139.9  535801  541560  5760         2.51
## 118 duplication  NC_001139.9  563821  568200  4380         1.90
## 122 duplication  NC_001140.6   40321   91080 50760         4.75
## 123 duplication  NC_001140.6  212461  219660  7200         2.64
## 127 duplication  NC_001140.6  544261  548460  4200         2.06
## 134 duplication  NC_001142.9  111541  113160  1620         1.91
## 136 duplication  NC_001142.9  472501  483840 11340         2.28
## 141 duplication  NC_001143.9  650641  651540   900         2.78
## 144 duplication  NC_001144.5  217801  220080  2280         2.30
## 146 duplication  NC_001144.5  451441  472560 21120        31.59
## 147 duplication  NC_001144.5  476341  481860  5520         2.37
## 149 duplication  NC_001144.5  593401  596700  3300         2.57
## 150 duplication  NC_001144.5  649981  655980  6000         2.22
## 154 duplication  NC_001145.3  184261  190020  5760         2.24
## 155 duplication  NC_001145.3  196621  202080  5460         2.54
## 160 duplication  NC_001146.8   24661   26940  2280         1.86
## 162 duplication  NC_001146.8   97321  100860  3540         2.37
## 165 duplication  NC_001146.8  520201  524280  4080         1.98
## 170 duplication  NC_001147.6  117961  123060  5100         2.75
## 171 duplication  NC_001147.6  594901  599940  5040         2.13
## 175 duplication  NC_001148.4   54961   61080  6120         2.22
## 181 duplication  NC_001148.4  804841  810240  5400         2.16
## 182 duplication  NC_001148.4  844501  856260 11760         2.13
lumpy_dup_filtered
##    svtype     chrom.1  start    end size
## 13    DUP NC_001145.3 908138 908616  478